Molecular cloning, complete nucleotide sequence, and gene structure of the provirus genome of a retrovirus produced in a human lymphoblastoid cell line

We found and characterized a type D retrovirus produced in a human lymphoblastoid cell line of B-cell lineage. The amino acid sequence of the N-terminal region of the purified major structural protein (PVTRSQGQVSSNTTGRASPHPDTHTIPE) revealed no high homology with any of the known retroviral amino acid sequences. We have cloned cDNA and the proviral genome integrated in the retrovirus-producing cells, and determined the complete nucleotide sequence and gene structures of the genome. The provirus genome is 8785 by long and has the structure of LTR- gag-prt-pol-env-LTR. The nucleotide sequences of the long terminal repeat (LTR) region and a part of the pol gene were closely related to the available sequences of squirrel monkey retrovirus (SMRV), and we designated this virus SMRV HLB, abbreviated as SMRV-H. The primer (tRNA 1,2 Lys)-binding sequence of SMRV-H (TGGCGCCCA GGACGTGGGGCTCGA) has a GG insertion, which is different from that of SMRV. The transmembrane protein of the 3′ terminal region of env gene contains an amino acid sequence of an immunosuppressive peptide (EVVLQNRRGLDLLTAEQGGICLALQE RCCFYANKS), in which R is unique in SMRV-H. The core sequence of the glucocorticoid regulatory element is found upstream of the two 42-bp imperfect repeats in the LTR. Sequences partially homologous to those of the rat IgE-binding protein gene are in gag and pol genes.